1 Biomark, Inc. 705 South 8th St., Boise, Idaho, 83702, USA

✉ Correspondence: Kevin E. See <>

1 Introduction

The decline of anadromous Pacific salmonids (Oncorhynchus spp.) across the Pacific Northwest, USA has prompted numerous actions aimed at reversing that trend. These actions are often categorized into four H’s – harvest modification, hatchery practices, hydro-system operations, and habitat rehabilitation. Problematically, there is substantial uncertainty regarding the degree of change that can be exerted across and within these categories, and what combination of changes will most cost-effectively and sustainably reduce mortality. Recently released “de-listing” criteria (NOAA 2016 need reference details) identified adult escapement targets at the population scale, providing a quantitative metric useful for evaluating the magnitude of survival improvements required. These abundance targets provide a benchmark against which habitat rehabilitation actions can be measured. Here we describe an approach for estimating life-stage specific habitat-based carrying capacity that can be used to quantitatively identify the magnitude of tributary habitat rehabilitation necessary to support de-listing. For perhaps the first time, the necessity of tributary habitat restoration can be demonstrated and the magnitude of required change can be placed in context with the other “H’s.”

Pacific salmon (Oncorhynchus spp.) species have experienced large declines in abundance throughout much of their range (Good et al. 2005). Declines can be partially attributed to lost or altered habitat, and thus, efforts to recover depleted salmon populations are replete with efforts to rehabilitate habitat used during the freshwater life-stages. Specifically, restoring salmonid carrying capacity through tributary rehabilitation actions has been identified as a key component of recovery efforts for salmon and steelhead (Oncorhynchus mykiss) in the Pacific Northwest, USA. Efforts have included increasing and improving existing habitat for both spawning adults and rearing juveniles. However, estimating habitat carrying capacity, both historic and contemporary, for various life-stages of Pacific salmon, as well as identifying important habitat characteristics that influence capacity, has been an ongoing but necessary challenge. Reliable methods to better understand fish-habitat relationships as well as to estimate capacity are necessary to identify those salmon and steelhead life-stages that are limited by habitat capacity, and further, to better direct tributary rehabilitation efforts.

Fausch et al. (1988) conducted a thorough review of attempts to predict the standing crop of fish from measurable habitat covariates from 1950 to 1985, and found that the vast majority of multiple linear regression models failed to detect a significant fish-habitat signal. Since that review, there has been progress in identifying some fish-habitat relationships for some salmonid species. Nickelson et al. (1992) found that juvenile coho were found in higher densities within pool habitat on the Oregon coast. Similarly, pool and pond densities were good predictors of coho smolt densities in western Washington (Sharma and Hilborn 2001). Bryant and Woodsmith (2009) found that juvenile coho abundance was positively related to large wood at the reach scale, however their results demonstrated a negative relationship between abundance and the number of pools. Braun and Reynolds (2011) similarly found positive associations between spawner densities of sockeye in the Fraser River and large wood, in addition to positive relationships to percent undercuts and percent pools. Densities of adult spawning coho were also higher in forested areas compared to urban or agricultural areas in the Snohomish River watershed (Pess et al. 2002). Mossop and Bradford (2006) examined juvenile Chinook in the Yukon river and found positive correlations between the log of fish density and several metrics related to residual pool dimensions and large woody debris abundance as well as a negative correlation between fish density and gradient. These studies were focused on predicting observed fish densities, not necessarily capacity, and for most of them the predictive extent is limited to a particular watershed. In addition, they all assumed some form of linear fish-habitat relationship, which often results in weak predictive power.

A number of studies have utilized other modeling approaches to elicit non-salmonid fish habitat relationships. Dunham et al. (2002) used a quantile regression approach to show a negative relationship between cutthroat trout densities and the width:depth ratio of a stream for the upper quantiles of trout density. The same approach was also used to map the potential extent of sole in the English Channel and southern North Sea (Eastwood et al. 2003). Machine learning models such as boosted regression trees and random forests have been used to examine species biomass, diversity and distribution for a number of different species (Pittman et al. 2009, Knudby et al. 2010, and Compton et al. 2012). The results from these studies highlight the importance and effectiveness of using techniques that can accommodate non-linear fish habitat relationships.

Most studies that have investigated fish habitat relationships focus on predicting a species’ distribution (presence / absence) or the average abundance or density, neither of which can be easily manipulated to predict carrying capacity. Further, many of these studies focus on only one or two measures of habitat. Sweka and Mackey (2010) estimated carrying capacity of Atlantic salmon parr using a quantile regression approach, but the only habitat covariate they included was cumulative drainage area. Traditionally, carrying capacity for salmonids has been estimated through stock-recruitment curves. However, this requires a long time-series of data with variety in the number of spawners which is not usually available (Cramer and Ackerman 2009).

In fisheries it has long been recognized that that biotic and abiotic factors limit productivity within and across life-stages. For the purposes of this paper, we define carrying capacity as the maximum number of individuals that can be supported given the quantity and quality of habitat available at a given life-stage. We assume that higher observed relative densities within a given life stage are a function of habitat quantity and quality. Furthermore, we assert that observed fish density is a poor predictor of habitat capacity owing to both a paucity of individuals, especially for threatened or endangered species, and the existence of unmeasured variables that may serve to limit capacity. To address this, we have developed a model to estimate juvenile rearing capacity for Pacific salmon in wadeable streams based on quantile regression forest (QRF) (Meinshausen 2006) models using measurements of fish abundance (and density) and habitat characteristics. QRF models combine the theory and justification of quantile regression modeling (Koenker and Bassett Jr 1978, Cade and Noon 2003) with the flexibility and framework of random forest models (Breiman 2001). They account for unmeasured variables and can be used to describe the entire distribution of predicted fish densities for a given set of habitat conditions, not just the mean expected density. Random forest models have been shown to outperform more standard parametric models in predicting fish-habitat relationships in other contexts (Knudby et al. 2010). Quantile regression forests share many of the benefits of random forest models, such as the ability to capture non-linear relationships between independent and dependent variables, naturally incorporate interactions between covariates, and work with untransformed data while being robust to outliers (Prasad et al. 2006). Meanwhile, quantile regression models have been used in a variety of ecological systems to estimate the effect of limiting factors (Terrell et al. 1996, Cade and Noon 2003).

The fish abundance/density and habitat data used to fit the QRF model presented here were available from seven watersheds within the interior Columbia River Basin (CRB), Pacific Northwest, USA. Within the interior CRB two major runs of Chinook salmon (Oncorhynchus tshawytscha; hereafter Chinook salmon) occur, stream-type (i.e., spring/summer run) and ocean-type (i.e., fall run), each characterized by different life history characteristics. Stream-type Chinook salmon enter freshwater earlier in the year, spawn in the upper reaches of a watershed, and the juveniles rear for up to 16 months in the freshwater before entering the ocean as smolts. Ocean-type Chinook salmon enter freshwater later (e.g. fall or winter) spawn lower in the watershed, and the juveniles may only spend between several weeks and six months in freshwater before migrating to the ocean. Here we focus on juvenile stream-type Chinook, in particular the summer rearing period during low flow. Data presented here are from Chinook salmon populations in the Upper Columbia River spring-run and Snake River spring/summer-run Evolutionary Significant Units (ESU). The Upper Columbia Spring-run ESU is listed as endangered under the Endangered Species Act, the Snake River Spring/Summer-run is listed as threatened (need citation).

In this study, we developed a QRF model to

  1. Identify measured habitat characteristics that are most strongly associated with observed Chinook salmon parr abundance and density,
  2. Use paired fish and habitat measurements to elicit fish-habitat relationships for those habitat characteristics identified as important for determining fish abundance and density,
  3. Predict contemporary habitat carrying capacity at all sites where the important habitat characteristics are measures (i.e., CHaMP sites within the Columbia River Basin),
  4. Extrapolate capacity predictions at CHaMP sites across a watershed using globally available attribute data to estimate the Chinook salmon parr capacity of that watershed, and
  5. Validate estimates of carrying capacity from QRF across multiple watersheds using independent estimates of capacity (e.g., spawner-recruit relationships).

This manuscript incorporates multiple measures of stream habitat to estimate fish-habitat relationships that encompass the collinear nature of most stream habitat metrics and can be used to predict carrying capacity. Our approach moves across several spatial scales, inferring fish-habitat relationships from detailed, localized habitat data and extrapolating capacity predictions across wide swaths of unsampled locations.

2 Methods

2.1 Study Site

Fish and habitat data used in our study were collected from eleven watersheds within the interior Columbia River Basin (CRB), Pacific Northwest, USA (Figure 8.1). The CRB covers more than 668,000 km\(^2\) draining large portions of Idaho, Oregon, and Washington, and smaller portions of Montana, Nevada, Utah, and Wyoming, as well as the southeastern portion of British Columbia. The habitat data used to populate the QRF model were collected by the Columbia Habitat Monitoring Program (CHaMP) (Volk et al. 2017) and were downloaded from https://www.champmonitoring.org. Data from the following 11 CHaMP watersheds were used in this study: Asotin, Entiat, John Day, Lemhi, Methow, Minam, South Fork Salmon, Tucannon, Upper Grande Ronde, Wenatchee and Yankee Fork. Juvenile density and abundance data were collected in a subset of 7 watersheds, at CHaMP survey reaches and were graciously provided by a number of projects, including the Integrated Status and Effectiveness Monitoring Project (Volk et al. 2017).

2.2 Data

CHaMP sites are 200 m to 500 m reaches within wadeable streams across select basins within the interior Columbia River Basin (CRB) selected based on a spatially balanced Generalized Random Tesselation Stratified (GRTS) sample selection algorithm (Stevens Jr and Olsen 1999, 2004). Habitat data within CHaMP sites were collected using the CHaMP protocol (CHaMP (Columbia Habitat Monitoring Program) 2016) which calls for field data collection during the low-flow period, typically from June through October. CHaMP habitat data include, but are not limited to, measurements describing channel complexity, channel units, disturbance, fish cover, large woody debris, riparian cover, size (depth, width, discharge), substrate, temperature, and water quality.

Juvenile fish surveys were conducted for sp/sum Chinook salmon parr during the summer low-flow season at many of the same sites surveyed using the CHaMP protocol. Survey methods included mark-recapture, three-pass removal sampling, two-pass removal sampling, and single-pass electrofishing, as well as snorkeling. These data were used to estimate sp/sum Chinook salmon parr abundance at all CHaMP sites where fish survey data were available. Three-pass removal estimates used the Carle-Strub estimator (Carle and Strub 1978), following advice from Hedger et al. (2013). Two-pass removal estimates used the estimator described by Seber (2002). Mark-recapture estimates used Chapman’s modified Lincoln-Peterson estimator (Chapman 1951) and were deemed valid if they met the criteria described in Robson and Regier (1964). These estimates were made using the removal function from the FSA package (Ogle et al. 2019) or the closedp.bc function from the Rcapture package (Rivest and Baillargeon 2019) in R software (R Core Team 2019). Snorkel counts were transformed to abundance estimates using paired snorkel-electrofishing sites to calibrate snorkel counts. For sites with invalid estimates or that were sampled with a single electrofishing pass, we developed an estimate of capture probability based on valid estimates, using a binomial generalized linear mixed effects model. Fixed effects were species, wetted width of the site, density of fish caught on the first pass and all possible two-way interactions. We included a random effect for fish crew / watershed. We used this model to predict abundances based on the number of fish caught on the first pass and any other covariates.

Abundance estimates at all sites were then translated into linear (parr/m) fish densities which were paired with the associated CHaMP habitat data. For sites that were sampled in multiple years, only the fish and habitat data from the year with the highest observed fish density was retained to avoid possible pseudo-replication, while remaining consistent with our goal of estimating carrying capacity. After removing duplicate samples, our initial dataset contained 313 unique sites with paired fish-habitat data (Table 7.1).

2.3 Habitat Covariate Selection

A key step in developing a QRF model to predict fish capacities was selecting the habitat covariates to include in the model. Random forest models naturally incorporate interactions between correlated covariates, which is essential since nearly all habitat variables are considered correlated to one degree or another, however, we aimed to avoid overly redundant variables (i.e., variables that measure similar aspects of the habitat). Further, including too many covariates can result in overfitting of the model (e.g., including as many covariates as data points).

To prevent overfitting, we pared down the more than 100 metrics generated by the CHaMP protocol describing the quantity and quality of fish habitat for each survey site. To assist in determining the habitat metrics to include in the QRF model, we used the Maximal Information-Based Nonparametric Exploration (MINE) class of statistics (Reshef et al. 2011) to determine those habitat characteristics (covariates) most highly associated with observed parr densities. We calculated the maximal information coefficient (MIC), using the R package minerva (Filosi et al. 2019), to measure the strength of the linear or non-linear association between two variables (Reshef et al. 2011). The MIC value between each of the measured habitat characteristics and parr density was used to inform decisions on which habitat covariates to include in the QRF parr capacity model.

Habitat metrics were first grouped into broad categories that included channel unit, complexity, cover, disturbance, riparian, size, substrate, temperature, water quality, and woody debris. Habitat metrics measuring volume and area were scaled to the wetted area of each site. Within each category, metrics were ranked according to their MIC value (Figure ??). Our strategy was to select one or two variables with the highest MIC score within each category so that covariates describe different aspects of rearing habitat (e.g., substrate, temperature, etc.). Additionally, we attempted to avoid covariates that were highly correlated (Figure ??) while including covariates that can be directly influenced by restoration actions or have been shown to impact salmonid juvenile density.

2.4 QRF Model Fit

Using the selected habitat covariates (Table 7.2), we fit a QRF model to predict habitat rearing capacity for spring/summer Chinook salmon parr, during summer months. After constructing a random forest, predictions of the mean response can be made by averaging the predictions of all trees, similar to the expected value predictions from a statistical regression model. However, the individual predictions from each tree, viewed collectively, describe the entire distribution of the predicted response, therefore, the random forest model can be used in the same way as other quantile regression methods to predict any quantile of the response. There were missing values for some habitat data; thus, any site visit with more than three missing covariates was removed from the dataset and the remaining missing habitat values were imputed using the missForest R package (Stekhoven and Bühlmann 2012, Stekhoven 2013). We fit the QRF models using the quantregForest function from the quantregForest package (Meinshausen 2017) in R software (R Core Team 2019), incorporating data from 309 records (paired fish-habitat data) and 18 habitat covariates (17.2 data points per covariate) (Table 7.2). The 90th quantile of the predicted distribution was used as a proxy for carrying capacity, following the suggestion of Sweka and Mackey (2010). We used the 90th quantile, rather than a higher quantile, to avoid using predictions that are aimed at the very upper tails of observed fish density, where the variability of predictions may be influenced by sample size issues.

After model fitting, the QRF model was then be used to predict capacity using measurements of the habitat covariates that were used to fit the model. In our case, this includes all sites within CHaMP basins in the interior Columbia River basin. For CHaMP sites that have been sampled in multiple years, we first calculated the mean for each habitat metric among years to make predictions. In total, we generated 543 predictions of spring/summer Chinook salmon parr capacity, during summer months, for the following basins: Entiat, Grande Ronde (including Minam), John Day, Lemhi, Methow, South Fork Salmon, Tucannon, Wenatchee and Yankee Fork.

2.5 Extrapolating to Other Sites

Using the QRF model, we predicted habitat capacity for juvenile rearing at all CHaMP sites within the interior Columbia River basin. To predict capacity at larger spatial scales, such as the watershed or population, we developed two extrapolation models (linear and areal capacity) based on globally available attributes (GAA) which were available for the entirety of tributary habitat utilized by a given population. The GAA data used here was taken from the list of GRTS master sample sites that the CHaMP sites were originally selected from (need citation). Possible covariates included temperature range, growing degree days, an index of disturbance, the square root of cumulative drainage area, stream power, slope, channel type and watershed (Table 7.3). The natural log of the CHaMP site capacity predictions was used as the response variable in a multiple linear regression model that incorporated the design weights of the CHaMP sites using the svyglm function from the survey package (Lumley 2019) in R software (R Core Team 2019). We fit two extrapolation models to each type of fish density, one that included watershed as covariate, for use in predicting capacity within CHaMP watersheds, and one that did not, for predicting everywhere else. We then made predictions of linear and areal capacity at all master sample sites throughout the interior CRB, generally spaced about one kilometer apart. Summaries of extrapolation model fit are shown in Table 7.4.

To summarize capacity at larger scales, the mean linear capacity (e.g., fish/m) of the master sample points along a particular tributary is multiplied by the length of that tributary. We first restricted the master sample points and lengths of streams to those with the domain of spring/summer Chinook, as defined by StreamNet (http://www.streamnet.org ) or using expert opinion from local biologists. The capacities of various tributaries could then be summed to estimate capacity at almost any spatial scale. However, for visualization, predictions of areal capacity (fish/m\(^2\)) were used.

2.6 Model Validation

Spawner-recruit data from several watersheds within the interior CRB were compiled to validate the extrapolated QRF estimates of spring/summer Chinook salmon parr capacity. Some watersheds had direct estimates of parr, while some had estimates of smolts and pre-smolts from rotary screw traps. For the latter, estimates of parr were calculated using estimates of over-winter survival. A series of spawner-recruit functions were then fit to this data including Beverton-Hold, Ricker, and hockey stick. Estimates of capacity were made from each of these spawner-recruit curves and compared with QRF estimates of capacity (Table 7.5, Figure 8.4).

3 Results

3.1 Habitat Covariate Selection

We categorized 145 habitat measurements collected using the CHaMP habitat protocol (CHaMP (Columbia Habitat Monitoring Program) 2016) into 11 habitat categories, and for each habitat covariate an MIC value was calculated based on the strength of association between the habitat covariate and the response variable, parr density (fish/m). We chose the following 18 CHaMP habitat covariates to fit the QRF model: channel unit frequency, thalweg depth CV, average wetted width to depth ratio, total fish cover, disturbance index, riparian ground cover, average thalweg depth, percent gravel, average substrate size (D50), percent substrate < 6mm, average hourly temperatures in the summer, maximum weekly average temperature, conductivity and frequency of large wood in the wetted channel (Table 7.2).

3.2 QRF Model

A QRF model was fit using 18 habitat covariates (Table 7.2) and the quantregForest package (Meinshausen 2006) in R (R Core Team 2019) and the 90th quantile of the predicted distribution was used as a proxy for carrying capacity. After model fit, we examined the relative importance of each habitat covariate included in the model (Figure 8.2). Moreover, QRF models allow one to visually examine the marginal effect of each habitat covariate on the quantile of interest using partial dependence plots (PDP). These plots show the marginal effect of changing a single habitat covariate while maintaining all other covariates at their mean values (Figure 8.3). However, given that many habitat metrics are somewhat correlated, these marginal effects are not independent of one another making the interpretation of partial dependence plots less straightforward. After model fitting, the QRF model was used to predict habitat capacity at all CHaMP sites within the interior Columbia River basin.

3.3 Extrapolating to Other Sites

3.4 Model Validation

Estimates of Chinook salmon parr capacity from the QRF and extrapolation models were comparable to independent estimates from spawner-recruit data (Table 7.5, Figure 8.4). QRF estimates had overlapping confidence intervals with one or more of the Beverton-Holt, Ricker, or hockey stick model estimates in each of the seven locations where comparisons were possible (Figure 8.4). Possible additional uncertainty was not accounted for in estimates of spawners-per-redd or spawners-per-parr, which would increase the confidence intervals around spawner-recruit estimates and the overlap among estimates. Correlations between parr capacity estimates from the QRF model and spawner-recruit models ranged from 0.905 (Beverton-Holt) to 0.965 (hockey stick). This favorable comparison provides strong validation, as the spawner-recruit estimates of Chinook salmon parr capacity were developed from completely independent datasets and using entirely different methods.

4 Discussion

4.1 A Tool To Estimate Habitat Capacity

In this study, we developed a novel approach to estimate the capacity of habitat to support Chinook salmon parr during summer months in wadeable streams. Our model can be used to quantify juvenile rearing capacity in Chinook salmon watersheds or populations and, in turn, quantify the magnitude of tributary habitat rehabilitation necessary to support Endangered Species Act (ESA) delisting. The QRF and extrapolation models presented here provide useful tools towards the prioritization, implementation, and evaluation of habitat restoration actions to recover depleted salmon populations. Moreover, the models presented here can be applied to multiple stages within the life cycle (e.g., parr, smolt, adult). Estimates of habitat carrying capacity for multiple life stages will allow biologists and managers to identify what life stage specific habitat is limiting. For example, QRF models and associated extrapolation models may demonstrate that habitat for a given population is sufficient to support adult spawning required for ESA delisting, but that juvenile capacity may not be sufficient to support those levels of adult spawning. In such a case, habitat restoration actions may be most cost-effectively and sustainably directed towards juvenile rearing habitat. Models to estimate habitat carrying capacity for multiple life stages will help to better direct habitat restoration actions.

4.2 What Models Are Currently Available?

Historically, fish-habitat relationship models have focused on species distribution or average abundance/density rather than directly addressing carrying capacity. The QRF approach employed here allows for the analysis of multiple correlated habitat metrics, often with non-linear relationships to fish density, in order to assess fish habitat relationships for higher quantiles that are assumed to represent carrying capacity.

4.3 Biological Expectations from QRF Model

The results of the QRF parr capacity model for spring/summer Chinook salmon meet many biological expectations.

4.4 Model Assumptions

Model assumptions should always be considered when interpreting results; the following assumptions were made when modeling habitat capacity using QRF methods. First, we assumed that sites with higher carrying capacity (i.e., ‘better’ habitat) contain more parr during fish surveys. Second, we assumed that carrying capacity is a function of habitat. Third, we assumed that estimates of parr densities from fish surveys are unbiased. Fourth, we assumed that at least some sites in our dataset were at or close to local carrying capacity at the site level. However, if this fourth assumption is not met, we will obtain a conservative estimate of carrying capacity (but the framework of the model is not wrong). Finally, we assumed that the 90th quantile of predictions at each CHaMP site is a reasonable proxy for carrying capacity. With insufficient data, it is difficult to get a well-defined estimate of higher quantiles because substantial amounts of data are necessary to define the tails of a distribution.

Assumptions we don’t need to make. Because QRF naturally incorporates non-linear relationships between predictor and response variables, we make no assumptions regarding the shape of fish-habitat relationships. Rather, fish-habitat relationships are estimated from the data with no a priori constraints. Moreover, we make no assumptions regarding correlations among habitat covariates; the random forest framework accounts for possible interactions between habitat metrics, so we don’t need to explicitly place them in the model.

4.5 Extrapolation Model

In addition to site-specific estimates of carrying capacity derived from paired fish-habitat data, our extrapolation model allows for analyses at larger extents, such as watershed and population level scales. This is an efficient technique to leverage existing relationships for meaningful management decisions.

While the Columbia River Basin is an excellent candidate for this type of extrapolation given the wealth of CHaMP data, application of this technique to areas with limited habitat data may be considerably more challenging. On-the-ground habitat data collection is costly, time-consuming, and often not reproducible; thereby limiting the effectiveness of this type of extrapolation. Additionally, the extrapolation model relies on Global Available Attribute (GAA) data which ….

Despite these considerations, we were able to leverage extensive datasets to produce carrying capacity estimates throughout the CRB that significantly increase or habitat restoration prioritization in a cost-effective manner.

4.6 The Future: Improving Habitat Data

Given the cost/extent of data necessary for QRF extrapolation in watersheds outside of the CRB, there is a pressing need to develop new tools for habitat analyses. Unmanned Aerial Systems (UAS or drone, commonly) are gaining popularity in wildlife and ecosystem monitoring for their ease of use, safety, accessibility, and cost-efficiency (Jones IV et al. 2006, Chabot and Bird 2015). UAS produce high-resolution, permanent data at a fraction of the cost of on-the-ground habitat sampling. Advances in imaging techniques (e.g., multispectral imaging) and post processing (e.g., automation of data collection from imagery) are already demonstrating increase in the efficiency and accuracy of data collection (Whitehead and Hugenholtz 2014, LeCun et al. 2015, Weinstein 2018).

Development of a standardized protocol to incorporate remotely sensed data (LiDAR, aerial imagery) into the collection of habitat metrics would greatly improve the broadscale application of QRF. Rapid advances drone technology further improves upon traditional habitat data collection by leveraging 1) sub-meter global navigation satellite system (GNSS) receivers; 2) cost-effective drone imagery collection, image stitching, and photogrammetry; and 3) semi-automated data post-processing. All data collection efforts would be georeferenced and topologically compatible to increase repeatability of methods and data collection locations; a primary criticism of previous CHaMP survey efforts. The implementation of such a protocol would circumvent the need to extrapolate by collecting data for individual channel units in a rapid manner using remote sensing technologies, thereby reducing labor, providing a cost-effective tool for habitat data collection supporting status and trend evaluation and model products to better inform habitat restoration prioritization and planning.

4.7 Conclusions and Next Steps

5 Acknowledgements

Model development efforts have been funded by the Bonneville Power Administration through projects 2003-017-00 and 2011-006-00 and by the Bureau of Reclamation and Idaho Office of Species Conservation through contract BOR002 16. Fish sampling work in the Lemhi River was also funded through the Idaho Office of Species Conservation through the Pacific Coast Salmon Recovery Fund. Special thanks to staff from the following agencies for providing data to calculate Chinook salmon parr abundance and density estimates: Columbia River Inter-Tribal Fish Commission, Oregon Department of Fish and Wildlife, and U.S. Fish and Wildlife Service. The models in this study were improved by conversations with Eric Buhle.

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7 Tables

Table 7.1: The number of unique sites, by watershed, with paired fish-habitat data used to populate the spring/summer Chinook salmon parr capacity QRF model
Watershed n Sites Percent
Entiat 61 19.7%
John Day 58 18.8%
Lemhi 33 10.7%
Minam 20 6.5%
South Fork Salmon 30 9.7%
Upper Grande Ronde 85 27.5%
Wenatchee 22 7.1%
Total 309 100.0%
Table 7.2: Habitat metrics and descriptions of metrics included in the QRF model to predict spring/summer Chinook salmon parr capacity (during summer months). Metrics are ranked in order of relative importance.
Rank Metric Metric Category Description
1 Wetted Width Integrated Size Average width of the wetted polygon for a site.
2 Discharge Size The sum of station discharge across all stations. Station discharge is calculated as depth x velocity x station increment for all stations except first and last. Station discharge for first and last station is 0.5 x station width x depth x velocity.
3 Avg. August Temperature Temperature Average predicted daily August temperature from NorWest, averaged across the years 2002-2011.
5 Fish Cover: None Cover Percent of channel unit with no fish cover.
6 Large Wood Frequency: Wetted Wood Number of large wood pieces per 100 meters within the wetted channel.
7 Fast Turbulent Frequency ChannelUnit Number of Fast Water Turbulent channel units per 100 meters.
8 Substrate Est: Coarse and Fine Gravel Substrate Percent of coarse and fine gravel (2-64 mm) within the wetted site area.
10 Large Wood Volume: Wetted Fast Turbulent Wood Total volume of large wood pieces within the wetted channel and Fast Water Turbulent channel units.
11 Channel Unit Frequency ChannelUnit Number of channel units per 100 meters.
12 Wetted Width CV Complexity Coefficient of Variation of the wetted channel width measured from cross-sections.
13 Sinuosity Complexity Ratio of the thalweg length to the straight line distance between the start and end points of the thalweg.
14 Slow Water Percent ChannelUnit Percent of wetted area identified asSlow Water/Pool channel units.
15 Percent Undercut by Area Cover The percent of the wetted channel area with undercut banks.
16 Fast NonTurbulent Frequency ChannelUnit Number of Fast Water Non-Turbulent channel units per 100 meters.
17 Wetted Channel Braidedness Complexity Ratio of the total length of the wetted mainstem channel plus side channels and the length of the mainstem channel.
18 Wetted Side Channel Percent By Area Complexity Ratio of the total area of side channel unit areas (both small and large) divided by the total area of channel unit polygons.
Table 7.3: Globally available attribute (GAA) habitat covariates used to extrapolate quantile regression forest (QRF) model predictions of spring/summer Chinook parr capacity to a larger scale (e.g., watershed, population).
Covariate Scale
TRange Reach (2 km)
Elev_M Site (300 m)
CHaMPsheds Reach (2 km)
NatPrin1 Watershed (HUC12)
DistPrin1 Watershed (HUC12)
SrtCumDrn Reach (2 km)
StrmPwr Reach (2 km)
Slp_NHD_v1 Reach (2 km)
Channel_Type Site (300 m)
WIDE_BF Site (300 m)
S2_02_11 Reach (2 km)
Table 7.4: Summary of extrapolation model fits, split by each of the responses and whether the extrapolation model used CHaMP watershed as a covariate or not.
Model Response \(r^2\) Adjusted \(r^2\)
CHaMP fish/m 0.495 0.466
non-CHaMP fish/m 0.349 0.325
CHaMP fish/m\(^2\) 0.542 0.516
non-CHaMP fish/m\(^2\) 0.404 0.383
Table 7.5: Estimates of parr capacity from both spawner-recruit data (Beverton-Holt, Ricker, hockey stick) and from extrapolated estimates of parr capacity from the quantile regression forest (QRF) model. Numbers in parentheses are coefficients of variation.
Population n Yrs Adult Data Parr Data Beverton Holt Ricker Hockey Stick QRF
Catherine Creek 20 Spawners RST 135,387 (0.269) 103,021 (0.141) 99,921 (0.21) 162,514 (0.183)
Chiwawa R. 20 Spawners Parr Surveys 248,586 (0.24) 166,139 (0.148) 174,216 (0.184) 207,928 (0.367)
Hayden Creek 7 Spawners RST 58,394 (0.244) 65,958 (0.195) 48,351 (0.174) 83,126 (0.278)
Minam River 14 Spawners RST 1,309,223 (2.18) 484,810 (1.444) 662,806 (1.726) 426,118 (0.225)
Tucannon River 27 Redds RST 4,791,131 (13.016) 1,234,653 (8.566) NA (NA) 548,400 (0.186)
Upper Grande Ronde River 8 Spawners RST 171,607 (0.388) 168,137 (0.298) 127,052 (0.317) 211,970 (0.211)
Upper Lemhi 7 Spawners RST 333,229 (0.322) 229,635 (0.212) 242,636 (0.252) 242,370 (0.234)

8 Figures

Watersheds with CHaMP habitat data. Watersheds in black also contain paired fish data. Watershed names are: 1 - Entiat, 2 - John Day, 3 - Lemhi, 4 - Methow, 5 - Minam, 6 - Secesh, 7 - South Fork Salmon, 8 - Tucannon, 9 - Upper Grande Ronde, 10 - Wenatchee, 11 - Yankee Fork.

Figure 8.1: Watersheds with CHaMP habitat data. Watersheds in black also contain paired fish data. Watershed names are: 1 - Entiat, 2 - John Day, 3 - Lemhi, 4 - Methow, 5 - Minam, 6 - Secesh, 7 - South Fork Salmon, 8 - Tucannon, 9 - Upper Grande Ronde, 10 - Wenatchee, 11 - Yankee Fork.

Relative importance of each habitat covariate included in the quantile regression forest (QRF) model to predict habitat capacity, during summer months, for spring/summer Chinook salmon parr

Figure 8.2: Relative importance of each habitat covariate included in the quantile regression forest (QRF) model to predict habitat capacity, during summer months, for spring/summer Chinook salmon parr

Partial dependence plots for the spring/summer Chinook salmon parr capacity quantile regression forest (QRF) model, depicting how parr capacity shifts as each habitat metric changes, assuming all other habitat metrics remain at their mean values. Tick marks along the X-axis depict observed values.

Figure 8.3: Partial dependence plots for the spring/summer Chinook salmon parr capacity quantile regression forest (QRF) model, depicting how parr capacity shifts as each habitat metric changes, assuming all other habitat metrics remain at their mean values. Tick marks along the X-axis depict observed values.

Spawner-recruit data from seven watersheds. Solid lines are the spawner-recruit curve, dashed lines are the estimated capacity, and shaded polygons depict the 95% confidence intervals of capacity. Blue corresponds to Beverton-Holt models, green to Ricker models, yellow to hockey stick models, and red to QRF estimates. The QRF solid curve is a Beverton-Holt model with the capacity parameter fixed to the QRF estimate of capacity.

Figure 8.4: Spawner-recruit data from seven watersheds. Solid lines are the spawner-recruit curve, dashed lines are the estimated capacity, and shaded polygons depict the 95% confidence intervals of capacity. Blue corresponds to Beverton-Holt models, green to Ricker models, yellow to hockey stick models, and red to QRF estimates. The QRF solid curve is a Beverton-Holt model with the capacity parameter fixed to the QRF estimate of capacity.

8.0.1 Colophon

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The current Git commit details are:

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